As described in the Introduction ("What causes Crohn's disease"), think again of Crohn's disease as an infected wound with a cause and a compounding problem (an infection). Without solving the compounding problem, we may never be able to "see" the cause.

We know that to cure a wound, we must first cure the super-imposed infection before the wound itself will begin to heal. With a normal wound, we know the types of bacteria that are likely to be causing the infection and therefore can select appropriate antibiotics. In Crohn's disease, we do not know what bacteria are infecting the "wound" or what is causing the wound.

In order to determine which bacteria are infecting the "wound" and what may be causing the "wound", it is necessary to look at the bacteria within the inflamed tissues rather than those on the mucosal surface or those in downstream fecal material as in most other studies.

It is our hypothesis that, by looking at the bacteria present within the inflamed and diseased tissues, we can identify those bacteria that are penetrating the intestinal barrier and causing the super-imposed infection and cesspool of bacteria. Such determinations may allow the application of targeted therapy leading to remission without the broad detrimental side effects of currently employed therapies. In addition, by identifying all the bacteria within the diseased tissue and comparing them to normal tissue we may be able to find what is actually causing that initiating wound.

The rationale for our approach is that the bacteria present within the diseased tissue are more likely to be relevant to the disease and inflammatory process than bacterial populations that are merely adherent to the mucosal surface or present in downstream fecal material. Our hypotheses and approach are innovative because we seek to define the microbiome within submucosal tissues of the diseased intestinal tract, representing a relevant bacterial population never before examined.
We have developed techniques that can effectively separate the mucosa (the superficial layer) and the submucosa (the underlying diseased tissue) from surgically resected intestinal tissues. By such methods, we are able to directly study the bacteria associated with the diseased tissues and not bacteria associated with the superficial layers of the gut.

Bacteria contain DNA segments known as the ribosomal DNA genes (rDNA) which contain both stable (identical in all bacteria) and variable (unique to certain bacteria) which allows the identification of all bacteria in a sample by genetic means. By exploiting these bacteria features by a method known as 16s metagenomic sequencing, and analyzing the DNA isolated from the submucosa (where the disease exists) to the superficial layers of the gut and to normal tissue (from the same patient and controls), we hope to define the bacteria responsible for the compounding infection and discover the underlying bacteria that are present in the cesspool and responsible for the initial "wound", i.e., the "trigger".

Identification of the bacteria that are compounding the disease and those bacteria that commonly translocate cross the intestinal barriers (and hence causing inflammation), we can design therapeutic strategies that can reduce and/or eliminate the compounding problem and provide patient relief without the use of immunosuppressive and anti-inflammatory agents.

Identification of the underlying bacterium that may be acting as the trigger and continuous insult to the immune system (and allowing the compounding infection to occur), will allow the development of targeted therapy that may, once and for all, result in a cure of Crohn's disease and not just remission.

Determining the presence of invasion and other disease-associated bacterial genes.
There are known bacterial genes that allow microbes to invade intestinal tissues and cause disease, but it is unknown how many related genes exist in unknown bacteria. By seeking to define the presence of these types of genes, we may be able to identify suspect organisms that are below normal detection methods or identify unknown organisms containing these or related genes. Identifying these genes.
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The intestinal barrier is there to prevent bacteria and other unwanted materials from passing through the intestinal wall and into the body. Although some bacteria do penetrate the intestinal barrier (known as translocation) in normal healthy individuals, In Crohn's disease there is a dramatic increase. Most bacteria have specific genes that allow them to translocate including adherence genes which allow the bacteria to adhere to the intestinal lining, and invasion genes which allow them to penetrate the intestinal barrier.

We have found that in Crohn's disease there is a disproportionate number of both adherence and invasion genes found within the submucosal tissues. These genes, however, did not correlate with any known bacterial species, suggesting the presence of yet unknown bacteria (see our article in the Journal of Clinical Gastroenterology). The presence of these adherence/invasion genes could account for the development of the cesspool and associated inflammation.

Since these genes are present in bacteriophages (bacterial viruses) and/or in plasmids (larger genes that are transferred between bacteria like a virus), it is possible that the "trigger" could simply be these bacteriophages/plasmids that get integrated into the normal gut bacteria thereby allowing a continuous influx of normal bacteria resulting in a cesspool and associated inflammation.

Our current efforts in this area involves improving our detection methods, reproducing our previous efforts in a larger patient population for statistical significance, and attempting to identify the types of organism that may ber harboring these adherence/invasion genes.

As previously noted in "The Cause of Crohn's disease" chapter, we now know that bacteria are involved and that Crohn's disease is related to an immune deficiency in the ability to recognize and kill certain types of bacteria. Based on this information, we believe it is inappropriate to treat patients with an immune deficiency with drugs that further interfere and diminish immune function. In addition, these anti-inflammatory and immunosuppressive drugs promote bacterial growth and proliferation rather than diminish it. Although these types of drugs do make the patient feel better, they do not solve the underlying problem and probably, in the long run, make the disease worse.

As such, most of our patients are treated with anti-bacterial drugs. Although anti-inflammatory are often given concurrently to provide relief from suffering, they are rarely given alone and patients are often able to stop taking immunosuppressive and anti-inflammatory drugs all together. Admittedly, not all patients respond to antibiotic therapy and, by looking at changes in bacterial gut populations, we hope to understand why some patients respond while other do not, why some patients seem only to go into remission (the disease comes back), and why some patients seem to be cured (long-standing remission).

In addition to the anti-bacterial therapy, we have teamed up with the pharmaceutical industry to promote the development and testing of drugs that stimulate the immune system (rather than suppress an already deficient system). We believe that such drugs, in combination with antibiotics, may lead to a cure of Crohn's disease. We hope to see some early clinical trials with these types of drugs in the near future.

The role of Mycobacterium paratuberculosis in Crohn's disease. Since the mid-1980's, there have been suggestions that an organism causing a similar disease in animals may be related to the cause of Crohn's disease. Despite the unequivocal association between M. paratuberculosis and Crohn's disease, a causal link has not been established and the notion that M. paratuberculosis may be involved in Crohn's disease is froth with controversy which greatly impedes progress.
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